R/splitOntologies.R

In mdgsa: Multi Dimensional Gene Set Analysis.

##splitOnotologies.r
##2013-04-07 dmontaner@cipf.es


##' @name splitOntologies
## @docType 
##' @author David Montaner \email{dmontaner@@cipf.es}
##' 
## @aliases 
##' 
##' @keywords split GO ontology
##' @seealso \code{\link{propagateGO}}, \code{\link{goLeaves}}
##'
##' @title Split an annotation list of GO terms by ontologies.
##'
##' @description
##' Splits an annotation list of GO terms according to the ontology
##' to which each term belongs to.
##' 
##' @details
##' Uses the information form the library GO.db.
##' If some id could not be associated to any ontology,
##' they are returned in an unknown ontology named "missing".
##'
##' @param annot annotation list.
##' @param na.rm if TRUE 'unknown' terms are excluded.
##' @param verbose verbose
##' 
##' @return A list with tree components, one for each ontology.
##' A fourth component is included is some term could not be allocated to
##' any of the three GO ontologies.
##' 
##' @import DBI
##' @import GO.db
##'
##' @examples
##'
##' getGOnames (c ("GO:0006915", "GO:0016020", "GO:0008152", "GO:0015288"))
##'
##' annot <- list ("GO:0006915" = c ("g1"),
##'                "GO:0016020" = c ("g2", "g3"),
##'                "GO:0008152" = c ("g1", "g2", "g3"),
##'                "GO:0015288" = c ("g4", "g5"))
##' annot
##' splitOntologies (annot)
##' 
##' @export

splitOntologies <- function (annot, na.rm = TRUE, verbose = TRUE) {
    
    if (verbose) {
        message ("Using GO.db version: ",
                 packageDescription ("GO.db", fields = "Version"))
    }
    
    ##go id to ontology
    micon <- GO_dbconn ()
    tabla <- dbReadTable (micon, "go_term")
    tabla <- tabla[,c("go_id", "ontology")]
    tabla <- tabla[tabla$go_id != "all",]
    
    go2ontology <- tabla[,"ontology"]
    names (go2ontology) <- tabla[,"go_id"]
    
    ##my go ids
    misgos <- names (annot)
    ##
    ontologia <- go2ontology[misgos]
    ontologia[is.na (ontologia)] <- "missing"
    table (ontologia, exclude = NULL)
    
    es.bp <- ontologia == "BP"
    es.cc <- ontologia == "CC"
    es.mf <- ontologia == "MF"
    es.na <- ontologia == "missing"
    
    res <- list ()
    res[["bp"]] <- annot[es.bp]
    res[["cc"]] <- annot[es.cc]
    res[["mf"]] <- annot[es.mf]
    
    if (sum (es.na) > 0) {
        message ("Some GO ids where not found, ")
        if (na.rm) {
            message ("they will be excluded from the list")
        } else {
            message ("they will go to the fourth element of the output list.")
            res[["missing"]] <- annot[es.na]
        }
    }

    ## OUTPUT
    res
}